4  Fish Dataset

Overview

The fish dataset contains visual survey data and associated metadata for reef-associated fish communities recorded during Pristine Seas expeditions. These data support ecological assessments of biomass, species richness, and community structure across sites, regions, and management zones.

All observations were collected using standardized SCUBA-based belt transects, following protocols for underwater visual surveys (UVS). At each station, trained observers recorded species identity, estimated total length, and abundance for all fishes encountered (see Methods for details).

The dataset follows the Pristine Seas data model: Site → Station → Observation → Summary, and is organized into the following related tables:

• fish.stations — One row per fish survey at a unique depth stratum per site. Includes diver, depth, number of transects, and effort metadata.
• fish.observations — One row per taxon observed at a station, including size, count, and calculated biomass.
• fish.biomass_by_taxa — A derived table with biomass estimates and ecological classifications (e.g., trophic group) aggregated by taxon and station.

Structure

Each fish record is linked to its corresponding site and station using ps_site_id and ps_station_id. This modular structure supports fine-scale ecological analysis and integration with other UVS methods such as benthic surveys and eDNA.

• Site — Location and environmental metadata (uvs_sites)
• Station — One fish survey at a site and depth (fish.stations)
• Observation — Fish records per transect (fish.observations)
• Summary — Aggregated biomass and community metrics (fish.biomass_by_taxa)

Table: fish.stations

This table contains one row per SCUBA-based fish survey conducted at a unique depth stratum within a site. Each row includes dive metadata, survey effort (e.g., number of transects, area surveyed), and optional ecological summaries such as species richness, abundance, and biomass (Table 4.1).

This table contains one row per SCUBA-based fish survey conducted at a unique depth stratum within a site. Each row includes dive metadata, survey effort (e.g., number of transects, area surveyed), and optional ecological summaries such as species richness, abundance, and biomass.

Stations are linked to the uvs_sites table via ps_site_id. The ps_station_id is constructed by appending the rounded depth (in meters) to the ps_site_id, followed by "m".

Example:

• ps_site_id: CHL_2024_uvs_001
  
• depth_m: 18.2
  
• ps_station_id: CHL_2024_uvs_001_18m

This station ID format is consistent across all underwater visual survey (UVS) methods in the Pristine Seas database, including fish, benthic cover, and eDNA surveys.

Standard depth strata for UVS methods

• Super shallow: ≤ 5 m
  
• Shallow: 5–15 m
  
• Deep: > 15 m

Table 4.1: fish.stations Table Schema

Field	Type	Required	Description
exp_id	STRING	TRUE	Expedition ID (e.g., CHL_2024)
ps_site_id	STRING	TRUE	Pristine Seas site ID shared by fish, benthic, and eDNA surveys
method	STRING	TRUE	Method name; always 'fish' for this table
ps_station_id	STRING	TRUE	Unique station ID (e.g., CHL_2024_uvs_001_18m)
diver	STRING	TRUE	Initials or name of the primary diver
depth_m	FLOAT	TRUE	Depth of the station in meters
depth_strata	STRING	TRUE	Depth stratum: super shallow (≤5 m), shallow (5–15 m), or deep (>15 m)
n_transects	INTEGER	TRUE	Number of transects surveyed at the station
area_m2	FLOAT	TRUE	Total area surveyed (in m²)
date	DATE	TRUE	Date of the fish survey
time	TIME	TRUE	Start time of the survey (local time)
location	STRING	TRUE	Name of the broader sampling area (e.g., reef or island)
sublocation	STRING	FALSE	Finer-scale site name within the location
habitat	STRING	TRUE	Habitat type: fore reef, back reef, etc.
exposure	STRING	TRUE	Exposure classification: windward, leeward, or lagoon
notes	STRING	FALSE	Optional comments or observations
n_species	INTEGER	FALSE	Number of species observed (optional summary)
abundance	INTEGER	FALSE	Estimated fish abundance (individuals per m², optional summary)
biomass	FLOAT	FALSE	Estimated total fish biomass (g/m², optional summary)

Table: fish.observations

This table contains one row per fish observation recorded on a single transect. Observations are organized by species, size, and count, and represent raw field data collected by trained divers using SCUBA-based underwater visual surveys (UVS). Each record includes the station and transect ID, species identity (taxon_id), estimated total length (length_cm), number of individuals observed (count), and standardized metrics for density and biomass (Table 4.2).

Each observation is linked to its corresponding station via ps_station_id, and to species-level metadata via taxon_id. All records from the same transect (A–C) within a station share the same ps_station_id and transect label.

The fields abundance and biomass are calculated post hoc using size-specific transect areas and taxon-specific length–weight parameters from the species reference table.

Transect dimensions based on fish size

• Fish ≥ 20 cm are counted on the outward swim within a 25 m × 4 m belt (100 m²)
  
• Fish < 20 cm are counted on the return swim within a 25 m × 2 m belt (50 m²) Note: In rare cases where transects deviate from the standard 25 m length, actual length should be recorded and used for calculating abundance and biomass.

⚠️ Each row represents a unique species–size–transect combination. Multiple size classes of the same species within a transect are recorded as separate rows.

Table 4.2: fish.observations Table Schema

Field	Type	Required	Description
obs_id	STRING	TRUE	Unique identifier for each observation (e.g., CHL_2024_uvs_001_18m_A_0001)
ps_station_id	STRING	TRUE	Unique ID of the station where the transect was conducted
transect	STRING	TRUE	Transect label within the station (e.g., A, B, C)
diver	STRING	TRUE	Initials or name of the diver who recorded the observation
taxon_id	STRING	TRUE	Unique identifier for the observed taxon (linked to species list)
scientific_name	STRING	TRUE	Scientific name of the observed species
length_cm	FLOAT	TRUE	Estimated total length (cm) of the individual or midpoint of size class
count	INTEGER	TRUE	Number of individuals observed at this length
abundance	FLOAT	FALSE	Estimated fish abundance (individuals per m²), standardized to transect area
biomass	FLOAT	FALSE	Estimated fish biomass (g/m²), standardized to transect area
notes	STRING	FALSE	Optional comments, behavioral notes, or uncertainty flags

Table: biomass_by_taxa

This table contains summarized fish biomass and abundance data by taxon and station, derived from raw observations. Each row represents the total estimated biomass (in grams per m²) and abundance (individuals per m²) for a given species or taxon recorded at a station.

Taxonomic and ecological fields (e.g., family, trophic group, functional group) are joined from the species reference list to support aggregation and visualization. This is the primary analysis-ready table for generating figures, summaries, and community structure plots.

⚠️ All biomass and abundance values are standardized to the appropriate transect area based on fish size, following UVS survey protocols.

Table 4.3: fish.biomass_by_taxa Table Schema

Field	Type	Required	Description
ps_station_id	STRING	TRUE	Unique Pristine Seas station ID (e.g., CHL_2024_uvs_001_18m)
exp_id	STRING	TRUE	Expedition ID associated with the station (e.g., CHL_2024)
location	STRING	TRUE	Broader sampling area (e.g., reef or island)
habitat	STRING	TRUE	Habitat type: fore reef, back reef, etc.
exposure	STRING	TRUE	Exposure classification: windward, leeward, or lagoon
depth_m	FLOAT	TRUE	Depth of the station in meters
depth_strata	STRING	TRUE	Depth stratum: super shallow, shallow, or deep
n_transects	INTEGER	TRUE	Number of transects surveyed at the station
taxon_id	STRING	TRUE	Unique identifier for the observed taxon (linked to species list)
scientific_name	STRING	TRUE	Scientific name of the taxon
family	STRING	FALSE	Taxonomic family (from species list)
trophic_group	STRING	FALSE	Ecological trophic group (e.g., herbivore, piscivore)
functional_group	STRING	FALSE	Functional classification (e.g., browser, planktivore)
abundance	FLOAT	TRUE	Estimated abundance (individuals per m²) of the taxon at the station
biomass	FLOAT	TRUE	Estimated biomass (grams per m²) of the taxon at the station
n_obs	INTEGER	FALSE	Number of observations (rows in `fish.observations`) contributing to this summary

QA/QC Procedures

This section describes the quality assurance and quality control (QA/QC) steps applied to the fish observation data:

• Species validation: All taxon_id values are validated against the curated species list. Unknown or ambiguous species IDs are flagged for manual review.
• Length outlier detection: Observations with length_cm outside of species-specific max/min values are flagged for review. This ensures that measurements are biologically realistic.
• Effort checks: Observation totals (count, abundance, biomass) are validated against the number of transects (n_transects) and expected effort per diver.
• Range enforcement: Fields like count, length_cm, abundance, and biomass are required to be non-negative and checked for reasonable ranges.
• Duplication check: Duplicate obs_id values and repeated species–length–transect combinations are flagged and removed.
• Cross-table validation: Ensure that ps_station_id exists in fish.stations and matches the corresponding metadata (e.g., habitat, exposure).
• Data completeness: Missing critical fields (e.g., taxon_id, length_cm) are flagged for review.
• Data summary checks: Post-processing checks ensure derived metrics like biomass and abundance fall within ecologically plausible ranges. Any unexpected values are flagged for further review.
• QA/QC flags: Each observation is tagged with a qaqc_flag to track its quality status: Pass, Warning, or Fail.

Data Access

• How to join with uvs_sites, species_lists, and other tables
• Tips for filtering by region, depth, or family
• Folded code examples (e.g., summarize richness or biomass)